Well it is "only" a script that clean (recursive delete):
- cache
- dalvik-cache
- some init.d scripts
- modules that might be left from older kernel
- cache
- dalvik-cache

So yes the system is empty because it is not to overwrite stuff with new things only to clean up some old stuff

BUT BE CAREFULL WITH IT AS IT CLEAN SOME INIT.D scripts THAT MIGHT OR MIGHT NOT BE USEFULL DEPENDING YOUR KERNEL AND THAT NEW KERNEL FLASH USUALLY ONLY WRITE THE KERNEL AND not the scripts from init.d.

So very good/usefull if your are sur/know your ROM and it custom init.d scripts (or backup your init.d scripts before doing it)

EDIT:
here a the init.d that this scripts try to remove
/system/etc/init.d/S70zipalign
/system/etc/init.d/S90scheduler
/system/etc/init.d/S99finish
/system/etc/init.d/89system_tweak
/system/etc/init.d/98system_tweak
/system/etc/init.d/S89system_tweak
/system/etc/init.d/S98system_tweak
/system/etc/init.d/S90screenstate_scaling
/system/etc/init.d/90screenstate_scaling
/system/etc/init.d/98screenstate_scaling
/system/etc/init.d/S98screenstate_scaling